Apparatus for capillary electrophoresis having an auxiliary electroosmotic pump. Following a conventional capillary electrophoresis system having a single power supply, a separation capillary, and an optical detector, a conductive membrane connects a second capillary to a second power supply. The second capillary and second power supply act together as an auxiliary electroosmotic pump capable of augmenting or inhibiting the bulk electroosmotic flow in the separation capillary. The apparatus can be used to optimize the stacking profile of the sample and, thus, improve the separation efficiencies for charged solutes.